If you're claiming that the laws of physics don't apply to the human body , go ahead. The calorie count on food is accurate enough to use when attemping to lose weight in a consistent manner.
It's not so much that the laws of physiscs don't apply as much as the satiety signals between protein vs. carbs. People who do a low carb diet properly spontaneously eat less calories because of the reduced amount of carbohydrate in the diet. The difference is that the protein is very satiating, so it will be hard to overeat, say, chicken breast, and no one would want to, and also on a proper low carb diet you have much less choices in what to eat.
So, yes, you are still observing the laws of physics, but you are also observing the laws of fat regulation, and by keeping insulin stable and not spiking blood glucose, there will be no reason to surge a large amount of insulin and cause fat to be stored. In fact, the opposite will be true, and in response to the protein and lower calories meals, glucagon will cause fat to be released from cells.
As I said before its not the only way to do it but it's the only the way that I've had success, for example. If you allow yourself to eat crap foods it tends to stall weight loss, or may never occur. This issue is the exact issue that Gary Taubes is trying to get the medical research community to look at.